Commit f60b23a0 authored by myron's avatar myron
Browse files

all non reression tests pass

parent 4c2139c3
......@@ -11,12 +11,13 @@ from XRStools import xrs_read, xrs_rois
import os
def main():
os.system("xz -dk mask.h5.xz --stdout > mask.h5")
os.system("xz -dk ../mask.h5.xz --stdout > mask.h5")
filter_path = "mask.h5:/FILTER_MASK/filter"
roi_scan_num = [245,246,247]
reference_scan_list = [245, 246, 247]
monitor_column = "izero/0.000001"
first_scan_num = 651
......@@ -56,7 +57,7 @@ def main():
"do_step_scalars" : False,
"do_step_interpolation_coefficients": True,
"do_step_interpolation_coefficients": False,
"do_step_finalise_for_fit": True
}
......@@ -138,6 +139,8 @@ def main():
)
main()
......@@ -5,7 +5,7 @@ import json
import os
import h5py
import math
from XRStools import tools_sequencer_interp
from XRStools import tools_sequencer_interp, xrs_rois, xrs_read
import os
def main():
os.system("xz -dk ../mask.h5.xz --stdout > mask.h5 ")
......@@ -37,26 +37,28 @@ def main():
["niter_global" , 3 ]
])
resynth_z_square = 0
resynth_z_square = 0.0
selected_rois = list(range(0,24)) + list( range(36,60) )
# selected_rois = list(range(0,24)) + list( range(36,60) )
selected_rois = list(range(24,36)) + list( range(60,72) )
scal_prod_use_optional_solution = True
scal_prod_use_optional_solution = False
volume_retrieval_beta = 6.0e-20
volume_retrieval_beta = 6.0e-1
volume_retrieval_niter = 100
steps_to_do = {
"do_step_make_roi": False,
"do_step_sample_extraction": True,
"do_step_sample_extraction": False,
"do_step_interpolation": False,
"do_step_extract_reference_scan": False,
"do_step_fit_reference_response": False,
"do_step_resynthetise_reference": False,
"do_step_scalars" : True,
"do_step_volume_retrieval" : False,
"do_step_scalars" : False,
"do_step_volume_retrieval" : True,
"do_step_put_all_in_one_stack" : True
}
......@@ -81,17 +83,19 @@ def main():
###### LOADING PEAKS SHIFTS
###### peaks_shifts = h5py.File("../peaks_positions_for_analysers.h5","r")["peaks_positions"][()]
###### assert( len(peaks_shifts) == 72)
roiob = xrs_rois.roi_object()
roiob.loadH5( roi_target_path )
elastic = xrs_read.Hydra( datadir )
elastic.set_roiObj( roiob )
elastic.get_compensation_factor( elastic_scan_for_peaks_shifts , method='sum')
el_dict = elastic.cenom_dict
Enominal = np.median( list( el_dict.values() ) )
peaks_shift = np.array([ el_dict["ROI%02d"%i] if ("ROI%02d"%i) in el_dict else nan for i in range 72 ] )
Enominal = np.median(peaks_shifts)
peaks_shifts-= Enominal
if steps_to_do["do_step_interpolation"]:
roiob = xrs_rois.roi_object()
roiob.loadH5( roi_target_path )
elastic = xrs_read.Hydra( datadir )
elastic.set_roiObj( roiob )
elastic.get_compensation_factor( elastic_scan_for_peaks_shifts , method='sum')
el_dict = elastic.cenom_dict
Enominal = np.median( list( el_dict.values() ) )
peaks_shifts = np.array([ el_dict["ROI%02d"%i] if ("ROI%02d"%i) in el_dict else nan for i in range( 72) ] )
Enominal = np.median(peaks_shifts)
peaks_shifts-= Enominal
else:
peaks_shifts = None
##############################################################
##########################################################################
......@@ -121,7 +125,7 @@ def main():
response_fit_options = response_fit_options,
resynthetised_reference_and_roi_target_file = resynthetised_reference_and_roi_target_file,
resynth_z_square = 0
resynth_z_square = 0,
selected_rois = selected_rois,
......@@ -135,6 +139,25 @@ def main():
if steps_to_do["do_step_put_all_in_one_stack"] :
volumefile = scalar_products_and_volume_target_file
h5file_root = h5py.File( volumefile ,"r+" )
scankeys = list( h5file_root.keys())
scankeys.sort()
volumes = []
for k in scankeys:
if k[:1]!="_":
continue
print( k)
if "volume" in h5file_root[k]:
volumes.append( h5file_root[k]["volume"] )
# volume = np.concatenate(volumes,axis=0)
volume = np.array(volumes)
h5py.File("concatenated_volume.h5","w")["volume"] = volume
h5file_root.close()
main()
......
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